maziyarpanahi/openmed

Your Data. Your Model. Your Hardware.

Turn clinical text into structured, de-identified insight on hardware you control.
OpenMed's core local runtime performs extraction and de-identification after required model artifacts are available. Model downloads, remote-provider adapters, telemetry-enabled paths, and user-configured integrations may use a network; review each model and dataset's terms.

PyPI package · Python 3.10+ · Model catalog · Research paper · Apache-2.0 SDK source

OpenMedKit · Apple Silicon / MLX · Android / ONNX Runtime Mobile · Browser / Transformers.js · Documentation

2,266 manifest entries  ·  35 model-backed PII languages  ·  Apache-2.0 SDK

English · 简体中文 · Español · Français · Deutsch · Italiano · Português · Nederlands · العربية · हिन्दी · తెలుగు · 日本語 · Türkçe · فارسی · Kiswahili

This iPhone example uses OpenMed's local runtime after the required model artifacts are available:

_{On iPhone via OpenMedKit: scan a clinical note, de-identify it, and extract clinical signals with Apple MLX processing locally in this configuration.}

_{Real-time PII de-identification: in this configured local workflow, the Nemotron Privacy Filter redacts names, addresses, IDs, and billing data from a synthetic clinical discharge packet. (All values shown are synthetic.)}

from openmed import analyze_text

result = analyze_text(
    "Patient started on imatinib for chronic myeloid leukemia.",
    model_name="disease_detection_superclinical",
)

for entity in result.entities:
    print(f"{entity.label:<12} {entity.text:<28} {entity.confidence:.2f}")
# DISEASE      chronic myeloid leukemia     0.98
# DRUG         imatinib                     0.95

A clinical NER model using the local runtime after its required artifacts are available.

From a source checkout, run the CPU-only synthetic contract demonstration:

python examples/v30_clinical_brief.py
# Optional: --model mlx, with the pinned model already cached on Apple silicon.

It de-identifies an embedded note, extracts and grounds a finding, then prints a cited brief, verdicts and a value-free review packet. NER/NLI providers are explicit synthetic test doubles, not trained-model or clinical validation. No external note input is accepted. The MLX option may refuse unsupported output; it never bypasses the guards. See the brief guide and demo script for the boundaries and local setup.

Start with the consumer agent-usage guide, or load the curated llms.txt documentation index. For callable local interfaces, use the MCP server, the typed tool registry, or the command-line interface. Ready-made cross-tool procedures live in the repository skills catalog.

• Curated model catalog: validate each model, license, and dataset for your use case.
• Safe Harbor-aligned configuration: can target the 18 identifier categories; expert deployment review remains required, and use of the SDK does not itself establish HIPAA compliance.
• Supported execution paths: CPU, CUDA, MLX, mobile, service, and browser adapters vary by environment and artifact.
• Deployment interfaces: Python, containers, services, and batch workflows require configuration and validation.
• SDK source: released under the Apache-2.0 License; model and dataset terms vary.

On supported Apple hardware, OpenMed can use MLX and OpenMedKit for local processing after required artifacts are available. Model acquisition and any user-configured remote integrations remain separate network boundaries.

// Add OpenMedKit to your app
dependencies: [
    .package(url: "https://github.com/maziyarpanahi/openmed.git", from: "3.0.0"),
]

Expected result: Swift Package Manager resolves OpenMedKit and makes import OpenMedKit available to your app target.

• MLX runtime for PII token classification, the Privacy Filter family, experimental GLiNER-family zero-shot tasks, and Python MLX-LM text generation with Laneformer; includes a CoreML fallback path for supported token-classification artifacts.
• Portable model naming where supported: an MLX model name can fall back to a matching PyTorch checkpoint when that mapping and artifact are available on non-Apple hardware.
• Python on Apple Silicon too: pip install --upgrade "openmed[mlx]".

Guides: MLX backend · OpenMedKit (Swift) · CoreML export

_{MLX on Apple Silicon: 24–33× faster than CPU PyTorch for the Privacy Filter: median latency per inference step, lower is better.}

OpenMedKit also ships as a native Android/Kotlin library for local document intake, OCR handoff, PII redaction, and token-classification inference through ONNX Runtime Mobile. Mobile model repositories include stable tensor names, dynamic sequence axes, tokenizer files, labels, and Android-ready fp32, fp16, INT8, and optional .ort outputs.

Add the scoped JitPack repository in settings.gradle.kts:

dependencyResolutionManagement {
    repositories {
        google()
        mavenCentral()
        maven {
            url = uri("https://jitpack.io")
            content { includeGroup("com.github.maziyarpanahi") }
        }
    }
}

Then use the immutable OpenMed v3.0.0 release:

dependencies {
    implementation("com.github.maziyarpanahi:openmed:v3.0.0")
}

See the Android installation guide for local builds and publishing details.

val model = OpenMedKit.fromDirectory(modelDir)
val entities = model.analyzeText("Patient Alice Nguyen was seen in cardiology.")

• Android ONNX profile emits model.onnx, model_fp16.onnx, model_int8.onnx, tokenizer assets, labels, and openmed-onnx.json.
• ORT Mobile support records the minimal-build operator configuration when ONNX Runtime conversion tooling is installed.
• Kotlin parity tests keep tokenizer offsets, span boundaries, and decoder output aligned with the Python runtime.

Guides: Android ONNX export · Android span parity · OpenMedKit Android

from openmed import OnnxModel

model = OnnxModel.from_pretrained(
    "OpenMed/OpenMed-PII-ClinicalE5-Small-33M-v1-onnx-android"
)
entities = model("Patient Alice Nguyen was seen in cardiology.")

npm install openmed @huggingface/transformers

import { loadOnnxModel } from "openmed";

const model = await loadOnnxModel(
  "OpenMed/OpenMed-PII-ClinicalE5-Small-33M-v1-onnx-android",
);
const entities = await model("Patient Alice Nguyen was seen in cardiology.");

flowchart LR
    A["Clinical text"] --> B["OpenMed<br/>(local-first)"]
    B --> C["Medical entities"]
    B --> D["PII detected"]
    B --> E["De-identified text"]
    style B fill:#0D6E6E,stroke:#0A5656,stroke-width:2px,color:#ffffff
    style C fill:#D6EBEB,stroke:#0D6E6E,color:#0E1116
    style D fill:#F7DCD8,stroke:#C5453A,color:#0E1116
    style E fill:#F5E27A,stroke:#A9A088,color:#0E1116

Rendered result: a local clinical-text pipeline that returns medical entities, PII findings, and de-identified text without sending data to a cloud API.

The skills/ catalog ships portable Agent Skills for on-device de-identification, clinical NER, FHIR export, evaluation, and the healthcare workflows around them. The same SKILL.md folders work in Claude Code, OpenAI Codex, OpenCode, and compatible agents; the installer uses each client's skills directory plus the cross-client ~/.agents/skills convention.

git clone https://github.com/maziyarpanahi/openmed && cd openmed
./install-skills.sh          # installs for Claude Code, Codex, OpenCode, and ~/.agents/skills

Then ask your agent for the pipeline using synthetic placeholders:

Build a local OpenMed pipeline that de-identifies a synthetic discharge note and extracts medication entities.

It loads the right skills and produces an on-device pipeline (openmed.deidentify(...) → openmed.analyze_text(...)). After the one-time model download, run that pipeline locally on real notes; do not paste real PHI into a cloud-hosted agent prompt. See the skills catalog and 30-second example.

# Core + Hugging Face runtime (Linux, macOS, Windows; CPU or CUDA)
pip install --upgrade "openmed[hf]"

# Add the REST service
pip install --upgrade "openmed[hf,service]"

# Apple Silicon acceleration (MLX)
pip install --upgrade "openmed[mlx]"

Expected result:

Successfully installed openmed-...

from openmed import analyze_text

result = analyze_text(
  "Patient received 75mg "
  "clopidogrel for NSTEMI.",
  model_name=
  "pharma_detection_superclinical",
)
print([(e.label, e.text) for e in result.entities])

[('DRUG', 'clopidogrel'), ('CONDITION', 'NSTEMI')]

python -m openmed.service.logging \
  --host 0.0.0.0 --port 8080

INFO:     Uvicorn running on http://0.0.0.0:8080
GET /health -> 200 OK

from openmed import BatchProcessor

p = BatchProcessor(
  model_name=
  "disease_detection_superclinical",
  group_entities=True,
)
results = p.process_texts([...])
print(len(results), sum(len(r.entities) for r in results))
print([(e.label, e.text) for e in results[0].entities[:1]])

3 7
[('DISEASE', 'leukemia')]

Browser / WebGPU

Package ONNX token-classification exports for in-browser inference through Transformers.js:

python -m openmed.onnx.convert \
  --model dslim/bert-base-NER \
  --output dist/example-onnx \
  --include-transformersjs

Example output:

Exported Transformers.js bundle to dist/example-onnx

import { pipeline } from "@huggingface/transformers";

const detector = await pipeline(
  "token-classification",
  "/models/openmed-pii/transformersjs",
  { device: "webgpu" },
);
const entities = await detector("Patient Casey Example called 212-555-0198.");
console.log(entities.slice(0, 2));

Example output:

[
  { entity: "NAME", word: "Casey Example", score: 0.99 },
  { entity: "PHONE", word: "212-555-0198", score: 0.98 },
]

Transformers.js export guide

Offline / air-gapped? Point model_name (or model_id) at a local directory and OpenMed loads it without contacting the Hugging Face Hub:

from openmed import OpenMedConfig, analyze_text

result = analyze_text(
    "Patient presents with chronic myeloid leukemia and Type 2 diabetes.",
    model_id="./models/OpenMed-NER-DiseaseDetect-SuperClinical-434M",
    config=OpenMedConfig(device="cpu"),
)
for entity in result.entities:
    print(f"{entity.label:<12} {entity.text:<28} {entity.confidence:.2f}")

Example output:

DISEASE      chronic myeloid leukemia     0.98
DISEASE      Type 2 diabetes              0.96

Because model_id points to a local directory, this example does not contact the Hugging Face Hub or any external model provider.

A curated registry of specialized medical NER models; browse the full catalog.

from openmed import extract_pii, deidentify

text = "Patient: John Doe, DOB: 01/15/1970, SSN: 123-45-6789"

# Extract PII with smart merging (prevents tokenization fragmentation)
result = extract_pii(text, model_name="pii_superclinical_large", use_smart_merging=True)
print([(e.label, e.text) for e in result.entities])

# De-identify with the method you need
print(deidentify(text, method="mask").deidentified_text)
print(deidentify(text, method="replace").deidentified_text)
print(deidentify(text, method="hash").deidentified_text)
print(deidentify(text, method="shift_dates", date_shift_days=180).deidentified_text)

Example output:

[('NAME', 'John Doe'), ('DATE', '01/15/1970'), ('SSN', '123-45-6789')]
Patient: [NAME], DOB: [DATE], SSN: [SSN]
Patient: Emily Chen, DOB: 03/22/1985, SSN: 456-78-9012
Patient: 6b8f...c4a1, DOB: 48b1...91de, SSN: 3f13...e912
Patient: John Doe, DOB: 07/14/1970, SSN: 123-45-6789

• Smart entity merging keeps 01/15/1970 whole instead of fragmenting it.
• Policy-aware pipelines add HIPAA/GDPR/research profiles, calibrated thresholds, signed audit reports, redaction previews, and minimum-necessary action selection.
• Faker-backed obfuscation with custom clinical-ID providers (CPF, CNPJ, BSN, NIR, Codice Fiscale, NIE, Aadhaar, Steuer-ID, NPI).
• HIPAA boundary: Safe Harbor-aligned categories and configurable thresholds are implementation aids; expert deployment review remains required, and SDK use alone does not establish compliance.
• Batch and streaming PII: extract or de-identify across many documents with BatchProcessor(operation="extract_pii" | "deidentify", batch_size=16) or incremental streaming helpers.

_{Batch processing: up to 3.3× higher throughput on CPU and 2.2× on MLX vs. one document at a time.}

Complete PII notebook · Smart merging · Anonymization quickstart

from openmed import extract_pii

text = "Patient Sarah Connor (DOB: 03/15/1985) at MRN 4471882."

variants = {
    "baseline": extract_pii(text, model_name="openai/privacy-filter"),
    "nemotron": extract_pii(text, model_name="OpenMed/privacy-filter-nemotron"),
    "mlx": extract_pii(text, model_name="OpenMed/privacy-filter-mlx"),
}
print([(e.label, e.text) for e in variants["baseline"].entities])

[('NAME', 'Sarah Connor'), ('DATE', '03/15/1985'), ('ID', '4471882')]

Extraction and de-identification support 42 supported PII language codes: am, ar, as, bn, cs, da, de, el, en, es, fa, fr, gu, he, hi, id, it, ja, kn, ko, ml, mr, nl, no, or, pa, pl, pt, ro, ru, sv, sw, ta, te, th, tr, uk, ur, vi, xh, zh, and zu, with the registry-backed PII model catalog in total. Russian routing currently uses a documented multilingual default-model placeholder. Bengali, Chinese, and Tamil have dedicated registry entries. An optional, user-configured Indic NER family can serve Assamese, Bengali, Gujarati, Hindi, Kannada, Malayalam, Marathi, Odia, Punjabi, Tamil, and Telugu. Set OPENMED_INDIC_NER_MODEL; OpenMed never bundles or automatically selects those optional weights. OpenMed also includes validator-backed national-ID coverage for additional ID-only locales such as Latvian, Slovak, Malay, Filipino, and Finnish.

See the per-language guide for each code's default PII model, Faker locale, and a before/after de-identification example.

python -c "from openmed import extract_pii; print([(e.label, e.text) for e in extract_pii('Dr. Pedro Almeida, CPF: 123.456.789-09, email: pedro@hospital.pt', lang='pt').entities])"

Example output:

[('NAME', 'Pedro Almeida'), ('ID', '123.456.789-09'), ('EMAIL', 'pedro@hospital.pt')]

from openmed import extract_pii

portuguese = extract_pii("Paciente: Pedro Almeida, CPF: 123.456.789-09, telefone: +351 912 345 678", lang="pt", use_smart_merging=True)
dutch      = extract_pii("Patiënt: Eva de Vries, BSN: 123456782, telefoon: +31 6 12345678", lang="nl", use_smart_merging=True)
hindi      = extract_pii("रोगी: अनीता शर्मा, फोन: +91 9876543210, पता: नई दिल्ली 110001", lang="hi", use_smart_merging=True)
arabic     = extract_pii("المريضة ليلى حسن، الهاتف +20 10 1234 5678، الرقم القومي 29801011234567.", lang="ar", use_smart_merging=True)
japanese   = extract_pii("患者 佐藤 花子、電話 +81 90 1234 5678、マイナンバー 1234 5678 9012.", lang="ja", use_smart_merging=True)
turkish    = extract_pii("Hasta Ayşe Yılmaz, telefon +90 532 123 45 67, TCKN 10000000146.", lang="tr", use_smart_merging=True)

for r in (portuguese, dutch, hindi, arabic, japanese, turkish):
    print([(e.label, e.text) for e in r.entities])

[('NAME', 'Pedro Almeida'), ('ID', '123.456.789-09'), ('PHONE', '+351 912 345 678')]
[('NAME', 'Eva de Vries'), ('ID', '123456782'), ('PHONE', '+31 6 12345678')]
[('NAME', 'अनीता शर्मा'), ('PHONE', '+91 9876543210'), ('ADDRESS', 'नई दिल्ली 110001')]
[('NAME', 'ليلى حسن'), ('PHONE', '+20 10 1234 5678'), ('ID', '29801011234567')]
[('NAME', '佐藤 花子'), ('PHONE', '+81 90 1234 5678'), ('ID', '1234 5678 9012')]
[('NAME', 'Ayşe Yılmaz'), ('PHONE', '+90 532 123 45 67'), ('ID', '10000000146')]

A Docker-friendly FastAPI service with request validation, shared pipeline preload, and unified error envelopes.

pip install --upgrade "openmed[hf,service]"
python -m openmed.service.logging --host 0.0.0.0 --port 8080

# or with Docker
docker build -t openmed:local .
docker run --rm -p 8080:8080 -e OPENMED_PROFILE=prod openmed:local

Example output:

INFO:     Uvicorn running on http://0.0.0.0:8080

curl -X POST http://127.0.0.1:8080/pii/extract \
  -H "Content-Type: application/json" \
  -d '{"text":"Paciente: Maria Garcia, DNI: 12345678Z","lang":"es"}'

Abbreviated example response:

{
  "text": "Paciente: Maria Garcia, DNI: 12345678Z",
  "entities": [
    {"text": "Maria Garcia", "label": "NAME", "confidence": 0.99, "start": 10, "end": 22},
    {"text": "12345678Z", "label": "ID", "confidence": 0.98, "start": 29, "end": 38}
  ],
  "model_name": "OpenMed/privacy-filter-multilingual"
}

Model lifecycle and service controls: free memory on demand with GET /models/loaded, POST /models/unload, and a keep_alive idle window; v1.8 also includes API-key/JWT auth, no-PHI request logging, tracing, gRPC, async jobs, webhooks, warm pools, dynamic batching, request coalescing, rate and concurrency limits, /livez, /readyz, and opt-in metrics:

OPENMED_SERVICE_KEEP_ALIVE=10m python -m openmed.service.logging --host 0.0.0.0 --port 8080
curl -X POST http://127.0.0.1:8080/models/unload -H "Content-Type: application/json" -d '{"all":true}'

Example response:

{
  "unloaded": true,
  "released": {"models": 1, "tokenizers": 1, "pipelines": 1},
  "active_models": {}
}

See the full REST service guide.

Full guides at openmed.life/docs.

AI agents can load the curated llms.txt index or the inlined llms-full.txt feed. Both are regenerated from the current documentation during every strict MkDocs build.

OpenMed's guardian is a fluffy Persian cat styled as a tiny Avicenna (Ibn Sina): the great Persian physician whose Canon of Medicine was the world's standard medical text for some 600 years. He keeps watch over the open book of medical knowledge, in a palette built around Persian turquoise (fīrūza): a local-first guardian for your most private data.

Contributions welcome: bug reports, feature requests, and PRs alike. Please read the Contributing guide and our Code of Conduct first.

• Open an issue
• Contributing guide · Code of Conduct · Maintainers · Security policy
• Translations welcome: help complete the other-language READMEs linked in the switcher at the top.

Found a vulnerability? OpenMed redacts PHI, so a redaction bypass or PHI/PII leak is a security issue: please report it privately, never as a public issue. See SECURITY.md for the responsible-disclosure policy and the private reporting form. Never include real patient data in a report.

OpenMed builds on excellent open-source work: particular thanks to OpenAI (the Privacy Filter architecture), NVIDIA (the Nemotron PII dataset), Hugging Face (transformers, Transformers.js & the model ecosystem), Apple (MLX), and the Faker maintainers.

The OpenMed SDK source is released under the Apache-2.0 License. Third-party asset notices are recorded in NOTICE.

@misc{panahi2025openmedneropensourcedomainadapted,
      title={OpenMed NER: Open-Source, Domain-Adapted State-of-the-Art Transformers for Biomedical NER Across 12 Public Datasets},
      author={Maziyar Panahi},
      year={2025},
      eprint={2508.01630},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2508.01630},
}

Expected result: BibTeX-compatible citation metadata for referencing OpenMed in papers, posters, and derived documentation.

If OpenMed is useful to you, a star helps others discover it.

5,400+ GitHub stars · 9 Oct 2026 snapshot